Merge pull request #885 from PathwayCommons/issue_876

Issue 876 and more.

Author: IgorRodchenkov

README.md

@@ -33,7 +33,7 @@ npm run start
 The following environment variables can be used to configure the server:
 
 - `NODE_ENV` : the environment mode, either `production` or `development` (default)
-- `PC_URL`  :   Pathway Commons web service endpoint URL (default: http://www.pathwaycommons.org/pc2/)
+- `PC_URL` : actual Pathway Commons web service endpoint URL (default: 'http://www.pathwaycommons.org/pc2/')
 - `PORT` : the port on which the server runs (default 3000)
 
 ### Configure RethinkDB
@@ -45,8 +45,8 @@ The following environment variables can be used to configure the server:
 ### Switching Pathway Commons Versions (release/other)
 
 If Pathway Commons data and files have been updated since this app's last built and run,
-or you simply want to connect to a different PC2 instance (and set PC_URL environment variable), 
-then the file `src/server/graph-generation/generic-physical-entities/generic-physical-entity-map.json` 
+or you simply want to connect to a different PC2 instance (don't forget to set PC_URL), 
+then the file `src/server/graph-generation/biopax-metadata/generic-physical-entity-map.json` 
 needs to be updated. Also, purge the RethinkDb db tables or simply switch the database.
 
 The following script downloads and processes physical_entities.json.gz file from Pathway Commons:

package-lock.json

@@ -23,7 +23,7 @@ const databases = [
   {database:'CAS', url:'http://identifiers.org/cas/', search:''},
   {database:'HPRD',url:'http://identifiers.org/hprd/',search:''},
   {database:'RefSeq',url:'http://identifiers.org/refseq/',search:''},
-  {database:'Pathway Commons',url:'http://pathwaycommons.org/pc2/',search:''},
+  {database:'Pathway Commons',url:null,search:''}, //TODO: was this PC_URL or xml:base (both should be configurable)?
   {database:'NCBI Gene',url:'http://identifiers.org/ncbigene/',search:''},
   {database:'Gene Cards',url:'http://identifiers.org/genecards/',search:''}
 ];

src/client/common/config.js

@@ -71,7 +71,8 @@ class Enrichment extends React.Component {
   }
 
   handleGenes( genes ) {
-    this.setState( { genes } );console.log(genes);
+    this.setState( { genes } );
+    // console.log(genes);
   }
 
   render() {

src/client/features/enrichment/index.js

@@ -40,6 +40,6 @@ echo "Processing $DATA"
 
 curl -s "$DATA" | gunzip -c | jq -cS 'map(select(.generic)) | reduce .[] as $o ({}; . + {($o.uri): {name: $o.name, label:$o.label, synonyms:$o."HGNC Symbol"}})' > generic-physical-entity-map.json
 
-mv generic-physical-entity-map.json ../../server/graph-generation/generic-physical-entities/
+mv generic-physical-entity-map.json ../../server/graph-generation/biopax-metadata/
 
 echo "\nUpdated generic-physical-entity-map.json"

src/scripts/generic-entity-mapping/update.sh

@@ -80,11 +80,11 @@ function getGraph(pcID, releaseID, connection, callback) {
   return db.handleResult(newerGraph, callback);
 }
 
-function getGraphFromPC(pcID, releaseID, connection) {
-  return getPathwayJson(pcID)
+function getGraphFromPC(pcURI, releaseID, connection) {
+  return getPathwayJson(pcURI)
     .then(result => {
       if (connection && result.pathwayMetadata) {
-        update.updateGraph(pcID, releaseID, result, connection);
+        update.updateGraph(pcURI, releaseID, result, connection);
       }
       return result;
     });

src/server/database/query.js

@@ -1,13 +1,16 @@
+const fs = require('fs');
 const metadataParser = require('./metadataParserJson');
 const _ = require('lodash');
-var biopaxFile = null;
+
+var biopaxMap = null;
+
 /**
- * 
+ *
  * @param {*} biopaxElement Metadata for an entity from BioPAX
  * @param {*} nodeType Is this a xref or entity?
  */
 function collectEntityMetadata(biopaxElement, nodeType = 'default'){
-  
+
   let result = [];
   //Collect relevant data on this node, and push it into output
   if (nodeType !== 'Reference') {
@@ -49,11 +52,11 @@ function collectEntityMetadata(biopaxElement, nodeType = 'default'){
 }
 
 /**
- * 
+ *
  * @param {*} entity Metadata for an entity in the network
  * @returns Tree array containing all metadata about the given entity
  */
-function buildBioPaxTree(entity) {  
+function buildBiopaxTree(entity) {
   let result = [];
 
   //make sure the metadata exists
@@ -81,28 +84,30 @@ function buildBioPaxTree(entity) {
     xrefList = _.concat(xrefList,[eref]);
 
   processXrefs(xrefList,eref,collectedData);
-  
+
   result.push([id,collectedData]);
   return result;
 }
 
 function processXrefs(xrefList,eref,collectedData){
-
   let erefXrefList = [];
 
   for (let i = 0; i < xrefList.length; i++) {
     //Check if this is a cross-reference or entity reference
+    //(- the last item (if eref is defined) is treated in a special way that
+    //TODO: saves a couple of lines but sacrifices clarity...)
     let keyName = 'Reference';
     if (i == (xrefList.length - 1) && eref)
       keyName = 'EntityReference';
 
     //Get Referenced element and make sure it's valid
-    let refElement = getElementFromBioPax(xrefList[i]); 
-    if (!(refElement))
+    let refElement = getByNodeId(xrefList[i], biopaxMap);
+    if (!(refElement)) {
       continue;
+    }
 
     //create list of xrefs for eref
-    if(keyName === "EntityReference"){
+    if(keyName === "EntityReference") {
       let erefXref = refElement['xref'];
       if(erefXref)
         if(typeof erefXref === 'string')
@@ -119,134 +124,109 @@ function processXrefs(xrefList,eref,collectedData){
   //almost identically to above
   for(let i=0;i<erefXrefList.length;i++){
     let keyName = 'Reference';
-    let refElement = getElementFromBioPax(erefXrefList[i]); 
-
-    if (!(refElement))
+    let refElement = getByNodeId(erefXrefList[i], biopaxMap);
+    if (!(refElement)) {
       continue;
+    }
 
     collectedData.push([keyName,collectEntityMetadata(refElement,keyName)]);
   }
 
 }
 
 /**
- * 
- * @param {*} id String representing potential BioPAX ID
- * @returns BioPAX metadata for that ID (if it exists) or null (if it doesn't)
+ * Gets an object from the given map by biopax URI or Cy node id;
+ * node id is mapped onto the biopax URI using several rules
+ * (knowing how the SBGN xml ids and CyJson node ids were generated).
+ *
+ * @param id String representing a BioPAX absolute URI or Cy node id
+ * @param  map Map/Object - biopax URI (string) to some objects map (e.g., to elements or metadata)
+ * @returns matching value from the Map (if it exists) or null
  */
-function getElementFromBioPax(id) {
+function getByNodeId(id, map) {
+  // shortcut
+  if(!id || !map)
+    return null;
 
-  //Remove any URL stuff from the ID, just like getProcessedBioPax
-  if (id.indexOf('http') !== -1 || id.indexOf('/') !== -1) {
-    var lastIndex = id.lastIndexOf('/');
-    id = id.substring(lastIndex + 1);
+  let bpe = (map instanceof Map) ? map.get(id) : map[id];
+  if (!bpe) {
+    //remove the last underscore and everything after, and search again (as generics/complex component ids
+    //are sometimes like ..Protein_4c4358ebaabf0f39e1e5325a4178d931_830703244edf74707f84842e080f965d)
+    id = id.substring(0, id.lastIndexOf("_"));
+    bpe = (map instanceof Map) ? map.get(id) : map[id];
   }
 
-  //Get element matching the ID
-  //make sure the ID isn't "" or null
-  if(id)
-    return biopaxFile.get(id);
-  else return null;
+  return (bpe) ? bpe : null;
 }
 
 /**
- * 
- * @param {*} nodeId node ID from Cytoscape network JSON
- * @returns Subtree containing BioPax metadata for the node
+ * Builds a URI-to-biopaxElement map from a biopax JSON-LD model.
+ * @param {*} biopaxJsonText String - BioPAX sub-network in JSON-LD format
+ * @returns `Map` containing BioPAX JSON objects
  */
-function matchCyIdToBiopax(nodeId) {
-
-  // The original entity IDs have been converted in the cytoscape network.
-  // Need to first find the original BioPAX entity ID, then collect metadata.
-
-  //Alot of this stuff is strange but it is ALL NECESSARY to correctly map the IDs
-
-  //Search for ID exactly as it appears
-  let searchTerm = getElementFromBioPax(nodeId);
-  if (searchTerm)
-    return searchTerm;
-  
-  //Search for ID after last underscore
-  searchTerm = getElementFromBioPax(nodeId.substring(nodeId.lastIndexOf("_") +1));
-  if (searchTerm)
-    return searchTerm;
-  
-
-  //Find index of second underscore
-  let i=0,index=null;
-  while(i<2 && index !==-1){
-    index = nodeId.indexOf("_", index +1);
-    i++;
-  }
-
-  //Remove extra identifiers appended by Cytoscape
-  //i.e. everything after the second underscore
-  let fixedNodeId = nodeId.substring(0,index);
-
-  //The last two methods won't work if there are no underscores in the ID
-  if (nodeId.indexOf('_') <= -1) 
-    return null;
-
-  //Search for ID in the first 2 underscores
-  searchTerm = getElementFromBioPax(fixedNodeId);
-  if (searchTerm)
-    return searchTerm;
+function getBiopaxMap(biopaxJsonText) {
 
-  //Search for ID in between first and second underscore
-  searchTerm = getElementFromBioPax(fixedNodeId.substring(fixedNodeId.lastIndexOf("_") +1));
-  if (searchTerm)
-    return searchTerm;
-
-  //Search Failed, return null
-  return null;
-}
-
-/**
- * 
- * @param {*} biopaxJsonText String containing BioPAX network metadata
- * @returns `Map` containing BioPAX network metadata
- */
-function getProcessedBioPax(biopaxJsonText) {
   //parse String into JSON object, rename '@id' property to 'pathid'
   const graph = JSON.parse(biopaxJsonText.replace(new RegExp('@id', 'g'), 'pathid'))['@graph'];
-  const biopaxElementMap = new Map();
 
-  //The 'pathid' property has a format like: http://pathwaycommons.org/pc2/someID
-  //Convert it to this format: someID, and make it the key for the map
-  for (const element of graph) {
-    const fullId = element['pathid'];
-    const lastIndex = fullId.lastIndexOf('/');
-    const subId = fullId.substring(lastIndex + 1);
+  const biopaxMap = new Map();
 
-    biopaxElementMap.set(subId, element);
+  //'pathid' is the absolute URI (URL, by design) of a biopax object, and so we use it as map key:
+  for (const element of graph) {
+    const uri = element['pathid'];
+    biopaxMap.set(uri, element);
   }
 
-  return biopaxElementMap;
+  return biopaxMap;
 }
 
+const getGenericPhysicalEntityMap = _.memoize(() => JSON.parse(
+  fs.readFileSync(__dirname + '/generic-physical-entity-map.json', 'utf-8')
+));
+
+
 /**
- * 
+ * Extracts additional BioPAX properties, for cy nodes,
+ * from the corresp. JSON-LD representation
+ * (these were missing from the initial SBGN-ML result, converted to CyJson.)
+ *
  * @param {*} biopaxJsonText String containing BioPAX metadata for the network
  * @param {*} nodes JSON object containing all the nodes in the network
  * @returns Processed metadata for each node in the network
  */
-function getBioPaxMetadata(biopaxJsonText, nodes) {
+function getBiopaxMetadata(biopaxJsonText, nodes) {
 
   //BioPAX metadata comes as a string, turn it into a Map
-  biopaxFile = getProcessedBioPax(biopaxJsonText);
+  biopaxMap = getBiopaxMap(biopaxJsonText);
 
   const nodeMetadataMap = {};
 
   //Iterate through nodes in Cy network, adding metadata to each
   nodes.forEach(node => {
-    const CyId = node.data.id;
-    //metadata for the Cytoscape node
-    const BiopaxData = matchCyIdToBiopax(CyId);
+    const bpe = getByNodeId(node.data.id, biopaxMap);
     //build the tree for metadata and add it to the map
-    nodeMetadataMap[CyId] = metadataParser(buildBioPaxTree(BiopaxData));
+    nodeMetadataMap[node.data.id] = metadataParser(buildBiopaxTree(bpe));
   });
 
   return nodeMetadataMap;
 }
 
-module.exports = { getProcessedBioPax, getBioPaxMetadata};
+/**
+ *
+ * @param nodes
+ */
+const getGeneSymbolsForGenericNodes = nodes => {
+  const nodeGeneSynonyms = {};
+  const genericPhysicalEntityMap = getGenericPhysicalEntityMap();
+
+  nodes.forEach(node => {
+    const genericPE = getByNodeId(node.data.id, genericPhysicalEntityMap);
+    const syns = _.get(genericPE, 'synonyms', []);
+    nodeGeneSynonyms[node.data.id] = syns;
+  });
+
+  return nodeGeneSynonyms;
+};
+
+
+module.exports = {getBiopaxMetadata, getGeneSymbolsForGenericNodes};